From e1f91fe0d1ab8c35cb5a5701399741cabfc91af0 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 19 Apr 2024 11:49:01 -0400 Subject: [PATCH] update tools and enable providing oh homozygous read coverage --- .../Assembly-Hifi-HiC-phasing-VGP4-tests.yml | 1 + .../Assembly-Hifi-HiC-phasing-VGP4.ga | 1044 +++++++++-------- .../CHANGELOG.md | 16 + 3 files changed, 604 insertions(+), 457 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 7d9d57906..55e219914 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -31,6 +31,7 @@ Bits for bloom filter: 32 Name for Haplotype 1: Hap1 Name for Haplotype 2: Hap2 + Homozygous Read Coverage: null outputs: Hifiasm HiC hap1: assert: diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index ca159e43b..5e7e37460 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "creator": [ { "class": "Organization", @@ -19,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.8", + "release": "0.1.9", "name": "Assembly-Hifi-HiC-phasing-VGP4", "steps": { "0": { @@ -131,37 +132,10 @@ "workflow_outputs": [] }, "4": { - "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", - "content_id": null, - "errors": null, - "id": 4, - "input_connections": {}, - "inputs": [ - { - "description": "GenomeScope model parameters generated by K-mer profiling workflow", - "name": "Genomescope Model Parameters" - } - ], - "label": "Genomescope Model Parameters", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 30.902209445950454, - "top": 431.8791830657761 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "0735f7ce-74e8-4ae0-8142-e6d2fd89c89e", - "when": null, - "workflow_outputs": [] - }, - "5": { "annotation": "Meryl database generated by K-mer profiling workflow", "content_id": null, "errors": null, - "id": 5, + "id": 4, "input_connections": {}, "inputs": [ { @@ -184,11 +158,11 @@ "when": null, "workflow_outputs": [] }, - "6": { + "5": { "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", "content_id": null, "errors": null, - "id": 6, + "id": 5, "input_connections": {}, "inputs": [ { @@ -209,13 +183,19 @@ "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6701efec-12e1-42db-86fb-13942ea9883a" + } + ] }, - "7": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 6, "input_connections": {}, "inputs": [ { @@ -236,13 +216,19 @@ "type": "parameter_input", "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c8ada6eb-8887-41a8-b1c4-4530ae2f5d3f" + } + ] }, - "8": { + "7": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -263,13 +249,19 @@ "type": "parameter_input", "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "72c45621-345f-4443-8d0e-af68962467e8" + } + ] }, - "9": { + "8": { "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", "content_id": null, "errors": null, - "id": 9, + "id": 8, "input_connections": {}, "inputs": [ { @@ -290,13 +282,19 @@ "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "474eb98c-2440-42c1-a684-ec9a8663de40" + } + ] }, - "10": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 10, + "id": 9, "input_connections": {}, "inputs": [ { @@ -317,13 +315,79 @@ "type": "data_input", "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "b835c7b0-d424-42d4-9445-86c694c1963a" + } + ] + }, + "10": { + "annotation": "If empty, read coverage will be estimated from the Genomescope parameters. 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"id": 41, + "id": 39, "output_name": "out_file1" } }, @@ -3364,6 +3494,6 @@ "VGP", "Reviewed" ], - "uuid": "d7c075ff-41a0-4dca-9fef-0133192aa9de", + "uuid": "b231c8cf-6047-4960-b332-7bf8a1e19223", "version": 2 -} +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index a5fcef992..9d2a2b28c 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,6 +1,22 @@ # Changelog +## [0.1.9] 2024-04-19 + +### Manual Updates + +- Add the option to provide Homozygous Read coverage parameter + +### Automatic update + +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4` + + ## [0.1.8] 2024-03-25 ### Manual update